A recent, comprehensive sequencing effort and subsequent evolutionary analysis of the Saccharomyces sensu stricto genus demonstrated that approximately 123 genes are rapidly evolving across the genus. The study of rapidly evolving genes is particularly relevant to human health as many of the rapidly evolving genes in the human genome are involved in host defense and immunity. And although evolutionary and genetic studies on humans have logistical limits, these same studies on members of the budding yeast Saccharomyces genus are much more tractable. The experiments proposed here will use physical and genetic interaction mapping to elucidate how the genome and proteome adapt to accommodate rapidly evolving genes in Saccharomyces cerevisiae and Saccharomyces bayanus. In the first aim, the physical interaction maps of a targeted set of three protein complexes, all containing a rapidly evolving subunit, will be determined in both S. cerevisiae and S. bayanus. In the second aim, a genetic interaction map will be constructed using epistatic mini-array profiling (E-MAP) technology, to identify synthetic genetic interactions between two identical sets of ~400 knockout strains, leading to the analysis of ~160,000 pair wise combinations of double knockouts in S. bayanus. These results will be compared to the extensive set of S. cerevisiae E-MAP data to identify differences in the genetic network connectivity of rapidly evolving genes in S. bayanus and S. cerevisiae. Taken together, these data will substantially expand our understanding of molecular adaptation to rapidly evolving genes among closely related species, and may inform future studies on how to target rapidly evolving genes in microbes so as to slow or eliminate the development of drug-resistant pathogens.